E-Biomed: Very important NIH Proposal

Stevan Harnad harnad at cogito.ecs.soton.ac.uk
Tue May 11 20:05:40 EST 1999


The following are comments on an NIH electronic archiving
proposal that could have enormous positive implications for
the scientific community. I strongly urge support for this
proposal. The full proposal is at:

<http://www.nih.gov/welcome/director/ebiomed/ebiomed.htm>

This extremely welcome and important initiative is deserving of
the strongest support. The following recommendations are made in
the interests of strengthening the proposal by clarifying some
crucial central aspects and modifying or eliminating some minor,
weaker aspects.

> E-BIOMED:
> A PROPOSAL FOR ELECTRONIC PUBLICATION IN THE BIOMEDICAL SCIENCES
> 
> Prologue
> 
> [T]he full potential of electronic communication has yet to be
> realized. The scientific community has made only sparing use thus far
> of the Internet as a means to publish scientific work and to distribute
> it widely and without significant barriers to access.

This generally accurate assessment of the current failure to exploit
the full potential of the Internet for scientific publication has one
prominent and extremely relevant and important exception. It would be
much more accurate as well as helpful to note this explicitly from the
outset, as this notable exception is very likely to be the model for
all the rest of the disciplines: 

Physics is the exception (and to some degree, mathematics). It is now
both an empirical and a historical fact that well over half of the
current physics (journal) literature is freely available online from
the Los Alamos Archive and its 14 mirror archives worldwide, and is
being used by perhaps 50,000 physicists a day.

<http://xxx.lanl.gov/cgi-bin/show_monthly_submissions>

It would be misleading in the extreme to describe this as "sparing
use"! Instead, it should be acknowledged that this has been a
revolutionary change in Physics, and if there were a way to extend it
to the other sciences (and the other learned disciplines) then the full
potential of electronic communication WOULD indeed be realized.

I stress this, because to pass over the revolution in Physics as if it
had not happened is not only to fail to give historical facts their due,
but it is to miss an important lesson for the rest of the scientific and
scholarly world in general, and the Biomedical Sciences in particular.

Insofar as the other disciplines are concerned, the paragraph quoted
above is a fair description of the status quo. The only bit of
ambiguity is the word "publish" in: "sparing use thus far of the
Internet as a means to publish scientific work and to distribute it
widely and without significant barriers to access."

"Publish" has two meanings in this context. One is "to make publicly
available in written form" (whether on paper, tape or screen), and the
other is "to appear in a refereed journal." It is best to distinguish
these two, as many people these days, usually well-meaning but extremely
under-informed about the nature of peer-reviewed publication, have been
suggesting that the latter (refereed publication) be watered down or
abandoned entirely in favour of the former (making publicly available
online). 

I think that such proposals (to modify peer review or substitute for
it the mere public online distribution of papers -- I am not speaking of
the E-biomed Proposal here, but of the need to distance it from such
proposals) are both (1) risky and (2) counterproductive

(1) Proposals to modify peer reviewed publication are based on armchair
speculation about publication and quality control, rather than on any
real experience with peer review or any tested alternatives to it
(there are none at the moment). Hence armchair proposals put the
quality and reliability of the research literature at risk without any
proven alternative, should any substantial number of well-meaning
people decide to go ahead and implement such proposals on any scale
without first carefully testing them out empirically.

Peer review can certainly benefit from study and improvement, and it is
indeed being studied empirically, but not by the armchair (or
screenside) tacticians. This research takes time and careful
experimental trials. And it is COMPLETELY INdependent of the medium --
paper or online -- in which the publication will take place. (The
online implementation of refereeing can be much faster and more
efficient, but this is just as true for paper publication, and indeed
more and more of classical peer review is being implemented online
already).

It is accordingly arbitrary and erroneous to couple changes in quality
control mechanism with changes in medium a priori. Not only is it
impossible to sort out the effect of two empirical variables if you
change both of them at the same time, but if quality control is
compromised by the implementation of untested alternatives, then the
effect could be misattributed to the online medium with which is was
coupled, thereby setting back the day when the learned community
finally realises the full benefits of a free online corpus. This is why
such proposals are not only risky (1), but counterproductive (2): They
can set back the online agenda instead of advancing it.

Change one variable at a time. If one's mission is to reform quality
control, then study and test new alternatives empirically. But if one's
mission is to make the current quality-controlled literature, such as it
is, freely available to everyone, everywhere online, rather than having
access to it continue to be obstructed by toll-barriers
(Subscription/Site-License/Pay-Per-View, S/L/P), then there is no need
either to await the reform of peer review, or to test whether free
access would be a good thing! The Los Alamos Archive has already proved
that it is a good thing; the world Physics community has already voted
with its eyes and fingers (and its papers, which are being self-archived
in the LANL Archive at an astounding and accelerating daily rate).

So: About "publishing" vs. "distributing": the picture is clear now:
Authors can now publicly self-archive their unrefereed preprints as well
as their refereed reprints. There is no reason to redefine
"publication." Let it continue to refer to acceptance by a refereed
journal. And let authors continue to submit all their papers to the
established refereed journals. But let them also self-archive them
(both as unrefereed preprints, and, once accepted, as refereed reprints)
in both their local institution's archive and in a global archive such
as LANL, with which E-biomed should COLLABORATE, emulating its
dramatically proven strengths, rather than trying to re-invent them 
or modify them a priori with untested incursions into either peer
review or publication. 

Preprint and reprint Archives are collective services to the world
scientific community; their efforts and resources should be pooled to
take advantage of economies of scale as well as to share the momentum
of the faster moving disciplines.

See: <http://www.library.yale.edu/~okerson/subversive.html>

> Informative and even visionary essays
> have explored this topic (see, for example, articles by
> Ginsparg <http://xxx.lanl.gov/blurb/pg96unesco.html>, 
> Walker <http://www.amsci.org/amsci/articles/98articles/Walker.html>, and
> Harnad [http://www.princeton.edu/~harnad/nature.html>,
> and references cited therein, as well as other recent proposals
> <http://library.caltech.edu/publications/scholarsforum> and
> <http://www.arl.org/newsltr/202/intro.html>).

I have done some critical commentary on both the Walker proposal and
the CalTech proposal. It all appears in the American Scientist
Archive:

<http://amsci-forum.amsci.org/archives/september-forum.html>

In a nutshell, Walker proposes financing free online eprints of
published journal articles out of journal offprint page charges; but
why should an author want to pay those charges if he can already
self-archive, in his local institutional archive and the Global Archive
(LANL/E-biomed), for free? There are some issues about how to pay for
the quality control, and page charges are indeed the right way, but not
author offprint charges levied by a journal that still blocks access
via S/L/P!

The ARL initiative is largely backing new forms of licensing. Inasmuch
as these retain the author's right to self-archive for free, they are
commendable; inasmuch as they help to preserve S/L/P barriers -- in the
form of L alone -- they are counterproductive.

The shared desideratum of all these initiatives is this:

    "It is easy to say what would be the ideal online resource for
    scholars and scientists: all papers in all fields, systematically
    interconnected, effortlessly accessible and rationally navigable
    from any researcher's desk worldwide, for free."

The way to arrive at this optimal outcome is through online
self-archiving by all authors (locally and globally). THAT is what
needs to be encouraged and facilitated. The rest will then take care of
itself (although we do need a rational transition strategy to cushion
the conversion of publishers from hybrid paper/online publication with
costs covered through S/L/P access barriers, to online-only publication
with the scaled down cost covered by up-front page charges, and the
literature then barrier-free for all).

> Before describing our proposal, it is important to acknowledge the
> strengths of the current system for published scientific work, because
> it has served the scientific community well for over 300 years.

I agree completely with the description that followed this passage, of
the value of the classical system of peer reviewed publication. I would
just add that even mentioning it risks introducing a red herring,
because there is no need whatsoever to tamper with this proven system of
quality control in order to achieve the optimal outcome above. 

> No proposal to change the way scientists publish their results and
> ideas should ignore these and other virtues of the current system. But
> we believe that current practices also have many liabilities and that
> these can be addressed by an evolutionary approach that need not
> threaten most of the benefits attributable to the print-based
> publication system that is now in place. More importantly, electronic
> publication can offer several remarkable benefits that could never be
> achieved through the current system. Many of these benefits depend on
> low-cost, barrier-free access by scientists to all of the contributions
> of their fellow scientists in a conveniently displayed electronic
> format.

I think that to formulate it as if realising the full potential of free
networked online communication somehow depended on modifying classical
quality control IN ANY WAY would be erroneous and would invite
misunderstanding. Free, public, self-archiving is a SUPPLEMENT to
classical peer review, not a SUBSTITUTE for it. We can have the optimal
outcome while keeping classical peer review 100% intact.

Nor is there any reason to talk about changing the way scientists
publish their results! The only thing wrong with the way they publish
their results is that they are not available to everyone online for
free. To achieve that, all they need to do is make them available to
everyone online for free! All "current practises" continue: Papers
continue to be submitted to the author's refereed journal of choice, as
before, they continue to be refereed, as before, and if accepted, they
continue to be published in the journal, as before. But IN ADDITION to
this, the author self-archives the unrefereed preprint at the beginning
of this quality-control process, and, still more important, also the
refereed reprints at the end of this quality-control process.

Here is where E-biomed plays its crucial role: in providing a reliable,
lasting archive for the author to self-archive in, one that authors can
trust, one with the authority and prestige to draw the entire
literature to it, and one that will support authors in exercising their
right to self-archive.

Unfortunately, the E-biomed proposal is a little vague on some of the
critical points, as I will try to show below. These critical points
concern the status of the established journals and classical peer
review. As for the rest of the above, it is all fine, feasible, and
desirable, but merely a SUPPLEMENT to current practises. This should be
made crystal clear, for attempting to change current practises,
particular along the lines of an untested alternative, can only induce
confusion and opposition.

> A proposal for E-biomed
> 
> In the plan presented here, the National Institutes of
> Health----through the National Center for Biotechnology Information, a
> component of the National Library of Medicine at the NIH---would
> facilitate a community-based effort to establish an electronic
> publishing site, called "E-biomed." It is important to emphasize at the
> outset that in no sense would the NIH operate as the owner or
> rule-maker for this enterprise. We are proposing this plan in an effort
> to accelerate much-needed public discussion of electronic publication
> in the United States and abroad and to provide the financial,
> technical, and administrative assistance to initiate such a program.

Here is the question to ask at this point, before misunderstandings
accumulate and wrong assumptions and inferences are made: 

Track A: Is E-biomed going to be a GLOBAL EPRINT ARCHIVE (like LANL), where
authors can self-archive their papers? If so, that is fine, highly
desirable, and should receive the highest encouragement. (And it should
pool resources, experience and expertise with LANL, which is already
supported by NSF/DOE and colossally successful

<http://xxx.lanl.gov/blurb/ups.html>

as well as with other current archiving initiatives such as the
Scholar's Forum

<http://library.caltech.edu/publications/scholarsforum> 

and NCSTRL <http://www.ncstrl.org/>

Track J: Or is E-biomed instead (or also, which is almost as bad) meant
as a rival to the established, peer-reviewed journals -- essentially a
RIVAL JOURNAL OR JOURNALS, providing peer review and certification? For
if so, you are again needlessly changing two empirical variables at
once:  (1) free online self-archiving (proven, good) and (2) new online
journals, with new, untested forms of quality control (again, risky,
and counterproductive, for we already have plenty of journals, and
there is no need to cast the new MEDIUM's lot with that of a new
journal or journals, competing with the established ones).

> In the plan we envision, E-biomed would transmit and maintain, in both
> permanent on-line and downloaded archives, reports in the many fields
> that constitute biomedical research, including clinical research, cell
> and molecular biology, medically-related behavioral research,
> bioengineering, and other disciplines allied with biology and medicine.

So far this is compatible with public, self-archiving, LANL-style,
Track J.

> The essential feature of the plan is simplified, instantaneous
> cost-free access by potential readers to E-biomed's entire content in a
> manner that permits each reader to pursue his or her own interests as
> productively as possible. We have attempted to endow the plan with the
> flexibility necessary for evolution as patterns of use become
> established and as new opportunities for enriching the system are
> proposed. And we suggest a mechanism for governance (the E-biomed
> Governing Board) that involves all of the parties concerned---the
> scientific community (readers and authors), editors, computer
> specialists, and funding agencies.

It is unclear what entities this passage refers to. Deliver a universal
Biology Archive of self-archived unrefereed preprints and refereed
reprints, LANL style and LANL scale (Track A), and the online frills
will take care of themselves. They are not the controversial part.
Don't overstructure this, especially on the basis of untested, unproven
structures: Deliver the free online literature and everything else will
follow suit.

> Copyright to reports posted in E-biomed would be retained by the
> authors, with the provision that intact versions would be freely
> available for transmission, downloading, and publication. Portions of
> reports could be reproduced only with the permission of the authors.

Of course authors should and will retain ownership of the intellectual
property they self-archive in E-biomed, just as when they self-archive
in LANL, or in CogPrints (the Archive I founded in order to extend the
LANL revolution to the Cognitive Sciences -- Psychology, Neuroscience,
Biology [!], Linguistics, Computer Science, Philosophy -- all destined
for eventual subsumption by LANL, once they attain critical mass).

<http://cogprints.soton.ac.uk/>

But this all goes without saying. (This report is a combination of
substantive and important steps toward achieving the optimal outcome
described above, together with solemn statements of the obvious! It
might fare better without the latter, I think.)

> Scientific reports in the E-biomed repository would be submitted
> through either of two mechanisms, as described in more detail in the
> succeeding sections. (i) Many reports would be submitted to editorial
> boards. These boards could be identical to those that represent
> current print journals or they might be composed of members of
> scientific societies or other groups approved by the E-biomed Governing
> Board. (ii) Other reports would be posted immediately in the E-biomed
> repository, prior to any conventional peer review, after passing a
> simple screen for appropriateness.

This is the core of the potential problem, and (i) is unfortunately
profoundly ambiguous:

If the "boards" are indeed IDENTICAL to those of current print
journals, then submitting to E-biomed would be tantamount to submitting
to one of those journals, which is perfectly fine, but then this is
merely the "overlay" system already being worked out at LANL: One can
submit to the American Physical Society (APS) journals by depositing
the preprint in the LANL Archive and specifying which journal it is
submitted to. The journal then proceeds with the refereeing of the
article, as usual (except online, which is faster and more efficient,
and is the way all journals are moving anyway).

If, however, the "boards" are not just the current journals (plus any
new startups that might fledge), but RIVALs to them, then this proposal
is conflating the establishment and encouragement of free public online
archives with the establishment of new online journals -- a different
proposition altogether, and definitely not one to which the fate of
online self-archiving should be linked, for reasons I described in my
critique of the CalTech proposal.

<http://www.cogsci.soton.ac.uk/~harnad/Hypermail/Author.Eprint.Archives/>

In contrast to (i), which concerns submitting to journals (old or new)
through the Archive, (ii) simply refers to self-archiving in the
archive. The latter is the generic category, however; the rest is just
about TAGGING (is this self-archived paper "U," an Unrefereed Preprint,
or is it "R," a Refereed Reprint? -- and if the latter, what Journal
"X"?). The rest is just about sectoring the Archive: If Journal X has
its own overlay, as the APS journals will have in LANL, then the author
can submit to it via E-bionet, and if a final draft is accepted, it can
receive an authentication tag not only from the author, but from the
publisher, certifying that it is indeed the published, final draft.
Search engines can then filter with that tag.

But underneath, generically, all we have is (i) self-archiving and tagging
of preprints and reprints by the author, and (ii) authorised overlays by the
journal publishers (whether the "new" rival journals, or the
established ones, but if it is to include the latter, you must work to
include them, as the APS was included in LANL: there will be
resistance, though, as Floyd Bloom's Science Editorial indicates; NIH,
however, can be a great asset in helping to persuade publishers to
collaborate rather than compete with the optimal outcome for research
and researchers).

<http://www.cogsci.soton.ac.uk/~harnad/science.html>

> (i) Submission to E-biomed through editorial boards
> 
> The first of the two mechanisms that authors would use to enter new
> scientific reports into the E-biomed database is closely aligned with
> current practice and retains scientific review as a prerequisite to
> publication. Authors would submit reports electronically to the central
> server, requesting review by the editorial board of an indicated
> journal in an appropriate field.

If this refers to the current established peer reviewed journals, it is
a splendid idea, exactly along the lines of the APS/LANL overlay. But
if it refers only to "new" journals one hopes to spawn along with the
Archive itself, it will only lead to trouble. Submitting for
publication through the Archive is only attractive to authors if they
can submit to the prestigious, high-impact journals of their choice --
not if it is to new, untested entities.

Work out agreements with a sufficient proportion of established
journals, as in the case of APS/LANL, and this will be a highly
attractive feature, and will hasten the success of the E-bionet
Archive. But provide only the promise of some sort of peer-reviewed
publication, and conflate it with the primary goal, which is
self-archiving itself, and the only result can be confusion and
resistance. This point MUST be clarified.

> If, after review, the report is accepted for publication in either its
> original or a revised form, the edited version would be posted
> immediately in E-biomed, and its title and list of authors would appear
> for a fixed period in the current table of contents for that journal.
> Later, it would continue to be accessible through the E-biomed search
> engine or through the journal's home page, annotated with the dates of
> submission, revision, and acceptance.

This has the same ambiguity as the prior passage. If we are talking
about new entities, prospects are bleak. If we are talking about the
established journals, then don't you first need their collaboration in
this? Will they agree to allowing their authors to self-archive their
preprints in the first place? They ought to agree, but currently many
explicitly do not (Science, and the New England Journal of Medicine are
examples that immediately come to mind). Rather than announce it as a
fait accompli, a priori, that established journals will allow their
authors to self-archive online preprints and to submit to the journal
via the Archive, I suggest you confirm this with a sufficient number of
them so that you have a viable and attractive package to offer
prospective self-archivers. (And if not, then drop the option for now.)

And it's not over with the unrefereed PREprint and the submission, for
the journals will also have to agree to having the refereed REprint
appear publicly for free in E-bionet. Again, they OUGHT to, and I don't
doubt that they eventually will, in view of the optimality of the
outcome for science and scientists, but we are not there yet, and there
are quite a few critical transition points we still need to get through
to get there. 

The APS have officially granted all their authors the right to
self-archive both their unrefereed preprints and their refereed
reprints; this is partly because the APS is a very enlightened and
progressive Learned Society, with an especially progressive and benign
Editor in Chief, Marty Blume; but it is also true that Physics is the
discipline which spawned LANL, and LANL is a fait accompli: Hence the
whole field was, de facto, archiving all its preprints and reprints
online already, well before any official overlay, collaboration, or
PERMISSION from APS.

That is why the path of a prior agreement with journals in Biology is a
much less sure one than one in which we set aside any promise of
offering the capability of submitting to refereed journals through the
E-bionet. Authors should simply be encouraged to self-archive all
preprints and reprints, as they did in LANL. The rest will take care of
itself. Waiting to build in, in advance, what LANL only gained by first
SUCCEEDING as a self-archive risks preventing E-biomed from hastening
us on the road to the optimal.

> If an editorial board judges the report unsuitable for inclusion among
> its own listings, the authors could resubmit the report for review by
> another board, defer further attempts to disseminate the findings, or
> publish in E-biomed through the alternative mechanism described in part
> (ii).

This passage is beginning to compound the ambiguity I mentioned above,
and to build it into a hypothetical structure with less and less basis in
reality.

What is the "editorial board" above? One of the established journals?
Then you are simply referring to conventional rejection and submission
to another journal. If you mean "new" entities, it is not at all clear
what all this is about. So I will assume you mean conventional
journals.  In that case, this passage is just stating the obvious: Of
course, as always, if one journal rejects your paper without requesting
revision and resubmission, and you still believe your paper worthy of
publication, you submit to another journal. Why restate the obvious in
this context?  Stick to what is relevant and unique to free online
self-archiving:  An unrefereed preprint can always be archived, tagged
and accessed as such: an unrefereed preprint, "U".

"Listings" somehow slipped in here too, and again it sounds like some
sort of fantasy to the effect that there is more to all this than just
self-archiving and journal submission: But journals publish, they do
not "list." They publish what their referees and editors judge to be
acceptable, and they tag it accordingly. The tag "JX" (eventually
authenticated by an official journal overlay but good enough for now if
the author so tags it) is all that's needed so that someone wanting to
search through (or to point an automating alerting agent at) only the
contents of Journal JX can do so, via the Archive.

("Content lists" and "issues" are outmoded papyrocentric concepts, not
relevant to the online medium.  To make this proposal credible, these
should be eliminated, as they only encourage others to think in old and
incompatible ways too!)

> Electronic publishing provides an opportunity to offer a third outcome
> to the review process, one that provides a novel solution to one of the
> most commonly encountered problems in current editorial practice. If a
> submitted report is deemed by an editorial board to be worthy of
> attention by some segment of the scientific community, but judged not
> to meet the criteria set for inclusion among a limited number of prime
> listings, the editorial board could still accommodate the report by
> choosing to maintain one or more additional listings. These additional
> listings might be grouped by specialty or simply designated as a
> larger, less exclusive version of the primary listing. Authors of
> reports that meet the criteria set for these listings---which, while
> less prestigious, still denote review and endorsement by the journal's
> editorial board --- could then elect immediate posting in E-biomed.

This begins to become more and more hypothetical. Current established
journals' only "listings" are the contents of the issues and volumes of
papers they have accepted. They do not have different "levels" of
acceptance. There do exist different levels of publication, however, and
these correspond to the established hierarchy of journals: They differ
in prestige, impact factor, rigour of peer review, and
specialty/generality. If we are talking here about established journals,
then these distinctions will continue to exist in the Archive, and will
be marked by the journal tag, JX, JY, just as they are now, in paper.
If a paper is not good enough for journal JX, it can be submitted to JY
etc. If it is eventually accepted, that will be its tag, and that will
be the journal that "lists" it.

But I am afraid that some "new" kinds of journals are being imagined
here, untested ones, based on probably incoherent notions such as
"listings" at different "levels" in the same "journal" by new kinds of
"editorial boards."

To get into this is to get into open-ended experimentation with quality
control and tagging -- a worthy long-term endeavour in itself, but not
relevant to the much bigger and more immediate objective of freeing the
literature for one and all online! There, it can only confuse and
retard, with armchair notions, when the path to the optimal outcome
(see your own first paragraph) is much clearer if unencumbered by these
irrelevant side-issues.

> (ii) Submission to E-biomed through the general repository
> 
> Authors would also have the option of entering scientific reports
> directly into the E-biomed repository without soliciting endorsement by
> the one of its editorial boards.

This is of course one of the primary functions of the archive: Apart
>From (a) submitting preprints for refereeing directly to journals via an
Archive Overlay, and apart from (b) self-archiving already refereed
reprints, one can also simply (c) self-archive unrefereed preprints.

That is exactly what it is; that is how it should be portrayed. The
importance of these functions, by the way, is exactly the reverse: The
most important is (c), for that is what a free, online, refereed
literature consists of. The unrefereed preprints (b) are important too,
and will speed communication and research in many cases. But the
overlay agreements with the journals (a) must await developments, is
not critical to the success or functions of the Archive, and certainly
must not be waited for (or promised in advance).

> Before publication in the database,
> each report would need to be approved by two individuals with
> appropriate credentials. These credentials, to be established by the
> E-biomed Governing Board, should be broad enough to include several
> thousands of scientists, but stringent enough to provide protection of
> the database from extraneous or outrageous material. (Such credentials
> might be membership on any approved editorial board or receipt of a
> research grant from a reputable funding source. The Governing Board
> would establish mechanisms to ensure that authors need not personally
> know two validators in order to have their submissions considered for
> deposition in E-biomed.)

This is potentially a bit confusing. Are there to be self-archived,
unrefereed preprints, with no one's endorsement, plus self-archived,
unrefereed preprints with some specialists' endorsement too? Fine, but
why add these arbitrary extra features a priori? Perhaps people will want
extra tags like this in calibrating their online browsing and reading:
They might want a restriction that is somewhere between looking only at
(1) papers that have been accepted by specific refereed journals, and
(3) papers that have been accepted by no journal at all, in the form of
(2) papers that have been vetted by an informal set of specialists.
(But (2) is only possible on the untested assumption that peers are
available to do more refereeing, and more levels of refereeing, than
they already do now -- for peer review, at every level, is a scarce
resource, and cannot be assumed to be compliant and available.)

But this all seems to be a pig-in-a-poke. We don't know whether peers
will do (2); we don't know whether authors will want (2); we don't know
whether readers will find (2) useful. Whatever is the case, (2) is a
an uncertain extra feature, and certainly not a precondition for
Archiving!

(And is all of Biomedical Science really just "several thousands of
scientists"?)

> Criteria for approval of reports must be sufficiently firm to guard
> against gross abuse of the E-biomed repository, but sufficiently
> flexible to permit rapid posting of virtually any legitimate work.

[Note added later: Paul Ginsparg has explained to me that this level of
vetting was meant to be very rudimentary, simply to filter out crank and
crackpot deposits. That is certainly a good idea and should be practised
by every Global Archive, but especially a Biomedical one, where
considerations of public health are involved.]

> At any time thereafter, the authors would be free to solicit review and
> endorsement from a specific editorial board as a means to provide
> greater prestige and visibility to a paper. Alternatively, interest in
> such reports could be enhanced by attaching to them informative
> commentaries written by other investigators.

UNLESS the above is simply stating the obvious -- which is that papers
self-archived in E-biomed as unrefereed preprints can also be submitted
for peer review to journals, possibly through Journal overlays in
E-biomed itself, and if accepted, can then appear in E-biomed also or
instead as refereed reprints -- this again sounds like needless
armchair fantasizing (neither necessary nor helpful to the Proposal, in
my opinion). It just mixes up what is attainable and important with
speculative scenarios that may or may not prove viable and useful some
day, but on which nothing now is or ought to be dependent.

[There is an echo here of a naive proposal we here over and over again,
that open commentary might somehow substitute for peer review: I would
suggest emphasizing that the Archive will contain self-archived
commentaries too, both unrefereed and refereed, and that these may be linked
to the articles, but don't associate the Proposal any more
closely with the quackish idea that spontaneous opinion polls could
serve as a basis for calibrating one's reading.]

A word: If the entire preprint and reprint literature were freely
available online, MUCH better ways of "publicising" one's work as well
as of finding the work of others will evolve. Don't try to constrain it
with the weak papyrocentric intuitions we have about this now, when the
literature is mostly still on paper, and the little that is online is
still behind financial firewalls.

> Initially, some authors might hesitate to try this route or might use
> it only to report information perceived to be difficult to publish in
> current journals. With experience, however, this mechanism is likely to
> become commonly employed because of its simplicity, flexibility, and
> speed; because electronic search engines are much more powerful than
> visual scanning of tables of contents to find relevant articles; and
> because other instruments (novel peer review mechanisms, appended
> commentaries, citation counts, and accession data) can be used to
> enhance the status and prominence of a report.

And all these potential powers of the online medium are just as valid
without these little speculative variants on peer review: They would be
there if we just got the classical preprint and reprint literature
online and freely available in E-biomed!

Commentaries are a whole new dimension:

    Harnad, S. (1979) Creative disagreement. The Sciences 19: 18 - 20.

    Harnad, S. (1984d) Commentaries, opinions and the growth of scientific
    knowledge. American Psychologist 39: 1497 - 1498.

    Harnad, S. (1998) Learned Inquiry and the Net:
    The Role of Peer Review, Peer Commentary and Copyright.
    Learned Publishing 4(11): 283-292
    http://citd.scar.utoronto.ca/EPub/talks/Harnad_Snider.html

> Open access to scientific reports and assembly of personalized journals

> E-biomed would allow each user to invent his or her own "virtual" or
> personalized journal, by downloading the reports he or she would like
> to read that week.

This too is an outmoded papyrocentic idea. Searching with the help of
tags and links is the online way, along with automatic personalized
alerting agents. Journals just become quality control tags; otherwise,
they are an outmoded concept.

> Improved format for publication of modern biology

Obviously, especially with online searchability and availability
of the entire corpus, including citation interlinking. 

> More rapid dissemination of scientific information
> 
> E-biomed would markedly speed up both the review and production
> processes currently used in scientific publishing.

Yes, immediate electronic availability speeds up availability itself,
and online peer review is faster than paper/mail. But referees' work
stacks will not get smaller, and there are still only 24 hours in their
days. As it stands, parts of this draft of the proposal would entail
using up MORE of the finite pool of scarce referee-hours doing things
that were not done in classical peer review. That could actually slow
the whole system down, if it really caught on (but there is reason to
doubt it would catch on, and no real reason to speculate about it one
way or the other, for the core purposes of this proposal).

> Moreover, many fewer reports would be sequentially reviewed by
> more than one editorial board in order to find a publishing outlet;

It is not at all clear why this proposal would lead to this, rather
than the opposite! But I strongly suggest that E-biomed stay out of the
peer review business (leave to the experts, who are doing well enough
already) and our of peer review reform (leave that to quality control
researchers, who can apply their tested findings to improving peer
review, once they have some findings!).

> Reduced costs
> 
> Scientific journals are inherently costly. The price of publication and
> distribution is presently levied on users in a variety of ways:
> subscriptions to libraries and individual readers for print and
> electronic versions; page charges to authors; and the time and labor
> required to maintain and use libraries. (The expenses currently
> incurred by institutions have recently been the subject of a much
> publicized scholarly report---accessible at
> http://jan.mannlib.cornell.edu/jps/jps.htm---and have even been held
> responsible for the decline in publication of academic monographs [see
> "The New Age of the Book" by Robert Darnham in The New York Review of
> Books, pp.5-7, March 18, 1999
> http://www.nybooks.com/nyrev/WWWarchdisplay.cgi?19990318005F].)
> 
> While our proposal cannot eliminate all of the costs associated with
> scientific publishing, movement to an electronic format is likely to
> reduce those costs dramatically (see an essay by Odlyzko for one
> account [http://www.research.att.com/~amo/doc/competition.
> cooperation.pdf]). The most crucial effect of cost reduction would be
> the opportunity to remove price as a barrier to individuals seeking any
> of the vast information deposited in E-biomed. It would also offer
> savings to individuals, laboratories, institutions, funding agencies,
> and the editors and publishers who move to electronic formats.

I think this proposal is extremely vague on the subject of cost and
cost-recovery. One CAN be much more specific about this subject, but for
E-biomed's immediate purposes there is no need at all to be more
specific -- in which case one should not claim to have done so:

This proposal is mute on (1) how to make the transition from paper to
online-only publication of journals, (2) how to recover the remaining
costs of quality control. I have tried to sketch out a way
<http://www.cogsci.soton.ac.uk/~harnad/nature.html> based on switching
to cost-recovery from up-front page-charges, but the promotion of
universal self-archiving by authors does not require a commitment to
any specific transition scenario. It is best, though, not to claim to
have helped solve cost-recovery problems that publishers are very
likely to energetically dispute!

E-Biomed is offering authors an archive to self-archive their
unrefereed and refereed papers. If they use it, this will, inter alia,
provide the refereed journal literature for free. Only then will we
have to worry about how to restructure journals to keep them afloat.
But E-biomed certainly does not have any proposal for this, so it would
be much better to drop any mention of a problem for which no solution
has been provided.

> Other possibilities
> 
> E-biomed is designed to evolve in ways that might affect the way we
> practice science.
> 
> o In an electronic publishing system, it is possible to engage
> electively in a more open reviewing process---one in which critiques of
> the scientific reports are accessible and possibly signed. This
> development, if widely accepted, could offer many benefits: more
> responsible reviews, an instructive and ongoing public conversation
> about published work, and career rewards for useful commentaries about
> work done by others. These reviews could be part of the vetting process
> that awards authors with a place on a table of contents of an E-biomed
> journal or they could be post-publication reviews appended to entries
> in the general E-biomed repository.

See references on the differences between Peer Review and Peer
Commentary, above. As in the other cases, the latter is a supplement to,
not a substitute for, the former. And there is an empirical literature
on the role of factors such as anonymity to supplement one's armchair
intuitions on such questions. The Proposal does not gain strength and
credibility but loses it when it is weighed down with unsupported
armchair speculations.

The substantive core of the E-biomed Proposal -- an archive for author
self-archiving -- is rock solid, feasible, and has strong empirical
support. The speculative reforms are best left for another project,
where there is no risk that they will drag down an already seaworthy
and urgently needed vessel.

> o Electronic publication could allow the amendment of reports,
> permitting authors to transmit additional information that might not
> warrant a separate report. Versions of reports containing supplementary
> information would be announced and clearly denoted as such, while the
> original versions are preserved as a 1.0 file for the historical record
> and downloaded for safekeeping

Yes, self-archiving includes the possibility of self-archiving of
updates and revised new editions of a paper, refereed and unrefereed,
and linking to them, as well as to comments and responses (and to papers
cited).

> The active E-biomed process might be accompanied by a much-needed
> effort to convert material already published on paper to digital text
> and image format, with hyper-linked citations. This additional
> initiative would ultimately allow all users of E-biomed to move
> seamlessly through the entire body of reported information in
> biomedical sciences. And it would also enhance scientific productivity
> and reduce burdens on library facilities.

Very useful and desirable; copyright questions to resolve, however. And
unless authors do their own scanning in and OCR for their own old
texts, the cost of centralized scanning and digitization could be used
as grounds for erecting permanent access-tolls to the retroactive
literature, which would be a great pity for all. An outright subsidy
would be preferable to reinstituting S/L/P for the pre-E-biomed
retrospective corpus.

[Of course living authors can and should scan in and self-archive all
their own retrospective work along with self-archiving their current
work.]

> o One further, less tangible benefit might also occur as a natural
> outcome of shared use of E-biomed: a heightened sense of community
> among biomedical scientists. This might be conducive to the adoption
> of uniform standards for sharing the data and providing access to the
> research tools described in E-biomed.

Certainly sharing a uniform, universal resource, with shared metadata
tags, will help to standardize and make the literature more
interoperable.

> How do we guarantee equity in the new system?
> 
> Although the current system of scientific publishing can be criticized
> for lapses of fairness, it has, in general, served us well. Thus any
> new system must be developed with concern for the ambitions of
> trainees, little-known scientists, or scientists at less prestigious
> institutions or foreign sites. Clearly, electronic communication has
> enormous advantages for people in all of these categories, because it
> is a democratizing force that makes distance and wealth nearly
> irrelevant. However, it is important to ensure that opportunities to
> enter reports into E-biomed are just as rich as the opportunities to
> access the reports filed by others. The editorial boards and the Board
> of Governors will need to give careful attention to this issue; for
> instance, it will be imperative to provide a means for any author,
> however remotely located or poorly known, to have access to two
> "members" of the system to validate reports submitted to the general
> repository.

This seems to be a pseudo-issue, unless the worry is about authors who
have no access to the Web at all. If quack-vetting is feasible at all,
there is no reason why any worthy paper should be at a disadvantage.
Much more relevant and important is the democratization provided by the
very existence of the online corpus, free for all. The access barriers
were the greatest inequity of all. (Best to put this in context, rather
than create needless pseudo-issues.)

> How should E-biomed get started?
> 
> o Does the plan make sense? Is it likely to achieve the benefits we
> ascribe to it? Are there other (better) ways to achieve them?

The self-archiving makes eminently good sense, and is a principle that
has already been tried and has had resounding success in Physics. Plenty
of empirical basis for extending it to Biology.

The speculations about peer review the vague promises about
collaboration with journals, old and new, are on much weaker ground,
completely unnecessary, and in my opinion considerably weaken the
proposal. The archiving has face validity; the refinements on peer
review and the relations with journals are just notional. Best to
completely uncouple the former from the latter, rather than dooming
them to a shared fate.

> o How should E-biomed be financed and managed? The NIH is prepared to
> provide funds and expertise to initiate the project. Should other
> funding agencies, in the U.S. and abroad, also support it? Or should
> funds be developed through other mechanisms, such as "submission
> charges" paid by authors?

Only the archiving facility needs support (not the refereeing system
innovations or the journal structures). This could be partnered with
NSF/DOE's LANL Archive, the Scholar's Forum initiative, and the ACM's
interoperable Gateway, NCSTRL, which will unify it with local
institutional Archiving Initiatives. One foreign partner could be the
UK's JISC eLib Electronic Libraries Programme, which is already
partnering with NSF and LANL. INSERM in France is contemplating taking
such steps too. The objective should be a worldwide, free
archive for the current research literature in all disciplines. The
first form this should take is an Archive for self-archiving by
authors. CogPrints (funded by JISC eLib) has adapted the LANL interface
to generalize it to other disciplines. This will be further adapted in
conjunction with a new JISC/NSF project to citation-interlink the
entire contents of the LANL Archive. NIH would be a welcome partner in
all this, and all resources could be shared.

> o What should be the composition of the E-biomed Governing Board? And
> how much authority should the Governing Board have over the functions
> of editorial boards that participate in E-biomed? What responsibilities
> should the Board have beyond developing rules of operation, producing
> an annual budget projection, negotiating with groups asking to
> establish editorial boards, and resolving disputes?

In my opinion, this is all irrelevant. E-biomed should not get into the
editorial-board and peer-review business. It needn't, and that has
nothing to do with the goal, which is to make the entire reprint and
preprint literature available online for free for all. I strongly
counsel you to drop all this refereeing-reform and journal-overseeing
if you really want to speed things on the road to the optimal.
Otherwise you will instead become involved interminably in Quixotic
reform proposals that have little to do with the goal that motivated
the whole undertaking, as described in your own Prologue!

> Once these and other questions have been considered, the NIH will
> publicize an appropriately modified proposal, assemble the Governing
> Board, and establish the E-biomed site with the Board's guidance.

I have been at so many meetings, in so many countries, in so many
disciplines in the past few years: Almost all of them want to make a
"policy statement" about what to do in the "electronic communication
revolution"; they want to make recommendations to governments; they
want to publicize in the general press. But none of them has a coherent
picture or plan. I just dissuaded the Commission of the German Learned
Societies from drafting a letter to the Science Minister triumphantly
announcing that the way of the future was "National Site Licensing
(NSL)," along the lines of BIDS in Britain. (Utter nonsense: NSL is a
Trojan Horse, one of the three horseman of the Trade Troika, S/L/P,
which are actually responsible for keeping this entire literature --
(the refereed journal literature), unique for being freely donated by
its authors -- separated from its readers by a spurious financial
firewall.)

Please don't now tell the NIH's governing Board that the way to free
the literature is to set up all kinds of new pig-in-poke reviewing and
editorial structures, in the hope that editors/referees will
collaborate and that authors will prefer them! The real message is
simple: Provide the resources and incentive for universal
self-archiving of preprints and reprints, as NSF/LANL does with such
colossal success and utility, and the rest will take care of itself!

If you want a model, and proof of principle and practise, just copy (or
better, collaborate with) LANL!

> Summary
> 
> The advent of the electronic age and the rise of the Internet offer an
> unprecedented opportunity to change scientific publishing in ways that
> could improve on virtually all aspects of the current system. The NIH
> has addressed this opportunity by proposing a new system, E-biomed,
> that has many advantages over the existing means of disseminating
> research findings: open access, greater speed, reduced cost, and
> enhanced depth of presentation. We now welcome constructive comments
> from the scientific community, with the intention of putting a suitably
> revised plan into operation in the near future.

All these virtues are already there, demonstrated and realised, in
LANL. Don't take something known that works astoundingly well, and turn
it into something unknown that may not work at all, by getting it mixed
up with notional peer review reform, with which it has no intrinsic
connection.

[For those who are impatient to start archiving your papers already,
you can do so at: <<http://cogprints.soton.ac.uk/>]

--------------------------------------------------------------------
Stevan Harnad                     harnad at cogsci.soton.ac.uk
Professor of Cognitive Science    harnad at princeton.edu
Department of Electronics and     phone: +44 1703 592-582
Computer Science                  fax:   +44 1703 592-865
University of Southampton         http://www.cogsci.soton.ac.uk/~harnad/
Highfield, Southampton            http://www.princeton.edu/~harnad/
SO17 1BJ  UNITED KINGDOM           ftp://ftp.princeton.edu/pub/harnad/



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